DuckDBDataFrame
This is the development version of DuckDBDataFrame; to use it, please install the devel version of Bioconductor.
DuckDB-Backed DataFrame and Table Structures
Bioconductor version: Development (3.24)
Provides DuckDB-backed implementations of core tabular data structures including DuckDBTable, DuckDBDataFrame, and DuckDBColumn. These classes extend Bioconductor's S4Vectors framework to enable efficient, out-of-memory operations on large tabular datasets using DuckDB's analytical database engine. The package includes SQL function discovery, connection management, and support for list columns and embeddings stored in ARRAY[] columns.
Author: Patrick Aboyoun [aut, cre], Genentech, Inc. [cph]
Maintainer: Patrick Aboyoun <aboyounp at gene.com>
citation("DuckDBDataFrame")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("DuckDBDataFrame")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DuckDBDataFrame")| 1. Introduction to DuckDBDataFrame | HTML | R Script |
| 2. Design and extension of DuckDBDataFrame | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software |
| Version | 0.99.20 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0), methods, stats, bit64, S4Vectors, IRanges |
| Imports | tools, BiocGenerics, S4Arrays, SparseArray, DelayedArray, Matrix, DBI, rlang, dplyr, dbplyr, duckdb, arrow, tibble |
| System Requirements | |
| URL | https://github.com/Genentech/DuckDBDataFrame |
| Bug Reports | https://github.com/Genentech/DuckDBDataFrame/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DuckDBDataFrame_0.99.20.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | DuckDBDataFrame_0.99.20.tgz |
| macOS Binary (sonoma-arm64) | DuckDBDataFrame_0.99.20.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DuckDBDataFrame |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DuckDBDataFrame |
| Bioc Package Browser | https://code.bioconductor.org/browse/DuckDBDataFrame/ |
| Package Short Url | https://bioconductor.org/packages/DuckDBDataFrame/ |
| Package Downloads Report | Download Stats |